MOLECULAR DOCKING: A VALUABLE TOOL FOR DETERMINING THE TOXICITY OF METHYL MERCURY TO HUMANS
Abstract
Mercury, mainly in its form of methyl mercury (MeHg), is a heavy metal of high environmental and toxicological relevance, as it can compromise the physiology of organisms and generate various pathologies in animals. Even with several toxic effects known in animals, studies of toxicity in humans remain the most restricted among mammals, possibly due to ethical barriers. Despite the anatomical and physiological similarities between experimental and human models, divergences may occur, at the molecular level, about the patterns of interaction between toxic agents and target proteins. Thus, simulations in the computational environment, through molecular docking using exclusively human proteins, presents itself as an experimental advantage, bringing: precision of results, saving time and financial resources, in addition to contributing to the reduction of the use of animals in research. The aim of this study was to screen mercury toxicity through proteins related to human physiological systems using molecular docking methodology with AutoDock Vina. The binding energies, amino acid residues and number of residues were similar in all analyzed proteins, demonstrating the possible systemic toxicity of Mercury, due to the possibility of compromising the function of proteins related to the nervous, digestive, excretory, respiratory, and reproductive systems.
Downloads
Metrics
References
Berman, H. M, Westbrook, J, Feng, Z, Gilliland, G, Bhat, T.N, Weissig, H, Shindyalov, I.N, Bourne, P.E (2000) The protein data bank. Nucleic Acids Research28:235-242. https://doi.org/10.1093/nar/28.1.235
Bolton, E, Wang, Y, Thiessen, P.A, Bryant, S.H. (2008) PubChem: integrated platform of small molecules and biological activities. In: Wheeler RA, Spellmeyer DC (eds) Annual reports in computational chemistry. Oxford, UK, Elsevier, pp 217-241. https://doi.org/10.1016/S1574-1400(08)00012-1
Brandão, F, Cappello, T, Raimundo, J, Santos, M.A, Maisano, M, Mauceri, A, Pacheco, M, Pereira, P (2015) Unravelling the mechanisms of mercury hepatotoxicity in wild fish (Liza aurata) through a triad approach: bioaccumulation, metabolomic profiles and oxidative stress. Metallomics 7(9):1352-1363. https://doi.org/10.1039/c5mt00090d
Bridges, C. C, Zalups, R.K (2010). Transport of inorganic mercury and methylmercury in target tissues and organs. Journal of Toxicology and Environmental Health, Part B3(5):385-410. https://doi.org/10.1080/10937401003673750
Chan, H. M (2019) Advances in methylmercury toxicology and risk assessment. Toxics 7(2):20. https://doi.org/10.3390/toxics7020020
Chen X, Ji H, Yang W, Zhu B, Ding H (2016) Speciation and distribution of mercury in soils around gold mines located upstream of Miyun Reservoir, Beijing, China. Journal of Geochemical Exploration 163:1-9. https://doi.org/10.1016/j.gexplo.2016.01.015
Chen, B, Zhu, Y, Ye, S, Zhang, R (2018) Structure of the DNA-binding domain of human myelin-gene regulatory factor reveals its potential protein-DNA recognition mode. Journal of Structural Biology203(2):170-178. https://doi.org/10.1016/j.jsb.2018.04.007
Chen, Y. Z, Ung, C. Y (2001) Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand–protein inverse docking approach. Journal of Molecular Graphics and Modelling20(3):199–218. https://doi.org/10.1016/s1093-3263(01)00109-7
Clarkson TW (1993) Molecular and Ionic mimicry of toxic metals. Annual Review of Pharmacology and Toxicology 32:545-571. https://doi.org/10.1146/annurev.pa.33.040193.002553
Datta U, Schoenrock SE, Bubier JA, Bogue MA, Jentsch JD, Logan RW, Tarantino LM, Chesler EJ (2020) Prospects for finding the mechanisms of sex differences in addiction with human and model organism genetic analysis. Genes, Brain and Behavior19(3):e12645. https://doi.org/10.1111/gbb.12645.
EPA Environmental Protection Agency (2010) Mercury. http://www.epa.gov/mercury/about.htm>. Accessed 17 March 2021.
Farias LA, Fávaro DIT, Vasconcellos MBA. Determinação de mercúrio e metilmercúrio em amostras de cabelo e peixes. Revista Instituto Adolfo Lutz, São Paulo, 68(3):451-60,2009.
Freedman Bill (2021) Biomagnification. The Gale Encyclopedia of Science, edited by Katherine H. Nemeh and Jacqueline L. Longe, 6th ed., vol. 1, Gale, 2021, pp. 594-597.
Genchi G, Sinicropi M, Carocci A, Lauria G, Catalano A (2017) Mercury exposure and heart diseases. International Journal of Environmental Research and Public Health 14(1):74. http://dx.doi.org/10.3390/ijerph14010074.
Govindasamy M, Sriram B, Wang S-F, Chang Y-J, Rajabathar JR (2020) Highly sensitive determination of cancer toxic mercury ions in biological and human sustenance samples based on green and robust synthesized stannic oxide nanoparticles decorated reduced graphene oxide sheets. Analytica Chimica Acta 1137:181-190. https://doi.org/10.1016/j.aca.2020.09.014
Guo X, Yoshitomi H, Gao M, Qin L, Duan Y, Sun W, Xu T, Xie P, Zhou J, Huang L (2013) Guava leaf extracts promote glucose metabolism in SHRSP.Z-Leprfa/Izm rats by improving insulin resistance in skeletal muscle. Bmc Complementary and Alternative Medicine 13(1):1-10. https://doi.org/10.1186/1472-6882-13-52
Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR (2012) Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics 4:17. https://doi.org/10.1186/1758-2946-4-17
Haq QMR, Jan AT, Ali A (2011) Glutathione as an antioxidant in inorganic mercury induced nephrotoxicityJournal of Postgraduate Medicine 57(1):72-82. https://doi.org/10.4103/0022-3859.74298
Hetényi C, Spoel DVD (2002) Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Science 11(7):1729-1737. https://doi.org/10.1110/ps.0202302
Howard MJ, Fuller C, Broadhurst RW, Perham RN, Tang JG, Quinn J, Diamond AG, Yeaman SJ (1998) Three-dimensional structure of the major autoantigen in primary biliary cirrhosis. Gastroenterology 115(1):139-46. https://doi.org/10.1016/s0016-5085(98)70375-0.
IBAMA Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis (2021) Mercúrio Metálico. http://www.ibama.gov.br/areas-tematicas-qa/mercurio-metalico-v2>. Accessed 20 March 2021.
Ibrahim ATA, Banaee M, Sureda A (2019) Selenium protection against mercury toxicity on the male reproductive system of Clarias gariepinus. Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology 225:108583-108593. https://doi.org/10.1016/j.cbpc.2019.108583
Jahan S, Azad T, Ayub A, Ullah A, Afsar T, Almajwal A, Razak S (2019) Ameliorating potency of Chenopodium album Linn. and vitamin C against mercuric chloride-induced oxidative stress in testes of Sprague Dawley rats. Environmental Health and Preventive Medicine 24(1):1-10. https://doi.org/10.1186/s12199-019-0820-x
Jeong J, Kim H, Choi J (2019) In Silico Molecular Docking and In Vivo Validation with Caenorhabditis elegans to Discover Molecular Initiating Events in Adverse Outcome Pathway Framework: Case Study on Endocrine-Disrupting Chemicals with Estrogen and Androgen Receptors. International Journal of Molecular Sciences10;20(5):1209. doi: 10.3390/ijms20051209. PMID: 30857347; PMCID: PMC6429066.
Jeromiyas N, Elaiyappillai E, Kumar AS, Huang S-T, Mani V (2019) Bismuth nanoparticles decorated graphenated carbon nanotubes modified screen-printed electrode for mercury detection. Journal of the Taiwan Institute of Chemical Engineers 95:466-474. https://doi.org/10.1016/j.jtice.2018.08.030
Johnson NC, Manchester S, Sarin L, Gao Y, Kulaots I, Hurt RH (2008) Mercury vapor release from broken compact fluorescent lamps and in situ capture by new nanomaterial sorbents. Environmental Science & Technology 42(15):5772-5778. https://doi.org/10.1021/es8004392
Karplus PA, Schulz GE (1987) Refined structure of glutathione reductase at 1.54 A resolution. Journal Molecular Biology 195(3):701-729. https://doi.org/10.1016/0022-2836(87)90191-4
Kavanagh KL, Oppermann U. Crystal structure of human glutathione peroxidase 7. https://doi.org/10.2210/pdb2P31/pdb. https://www.rcsb.org/structure/2P31. Accessed 19 april 2021.
Kim B, Kim S, Jin MS (2018) Crystal structure of the human glial fibrillary acidic protein 1B domain. Biochemical and Biophysical Research Communications503(4):2899-2905. https://doi.org/10.1016/j.bbrc.2018.08.066.
Kogularasu S, Akilarasan M, Chen S-M, Elaiyappillai E, Johnson PM, Chen T-W, Al-Hemaid FMA, Ali MA, Elshikh MS (2018) A comparative study on conventionally prepared MnFe2O4 nanospheres and template-synthesized novel MnFe2O4 nano-agglomerates as the electrodes for biosensing of mercury contaminations and supercapacitor applications. Electrochimica Acta 290:533-543. https://doi.org/10.1016/j.electacta.2018.09.028
Kursula P, Thorsell AG, Arrowsmith C, Berglund H, Edwards A, Ehn M, Flodin S, Graslund S, Hammarstrom M, Holmberg Schiavone L, Kotenyova T, Nilsson-Ehle P, Nordlund P, Nyman T, Ogg D, Persson C, Sagemark J, Stenmark P, Sundstrom M, van den Berg S, Weigelt J, Hallberg BM (2021) Crystal structure of human FABP1. https://doi.org/10.2210/pdb2F73/pdb. https://www.rcsb.org/structure/2F73. Accessed 19 april 2021.
Laskowski RA, Swindells MB (2011) LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling 51:2778-2786. https://doi.org/10.1021/ci200227u
Lavoie SP, Summers AO (2018) Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure. Bmc Genomics 19(1):1-10. https://doi.org/10.1186/s12864-017-4413-z
Li S, Shi M, Wan Y, Wang Y, Zhu M, Wang B, Zhan Y, Ran B, Wu C (2020) Inflammasome/NF-κB translocation inhibition via PPARγ agonist mitigates inorganic mercury induced nephrotoxicity. Ecotoxicology and Environmental Safety201:110801-110811. https://doi.org/10.1016/j.ecoenv.2020.110801
Liu Z, Liu Y, Zeng G, Shao B, Chen M, Li Z, Jiang Y, Liu Y, Zhang Y, Zhong H (2018) Application of molecular docking for the degradation of organic pollutants in the environmental remediation: A review. Chemosphere. Jul;203:139-150. doi: 10.1016/j.chemosphere.2018.03.179.
Lohren H, Blagojevic L, Fitkau R, Ebert F, Schildknecht S, Leist M, Schwerdtle T (2015) Toxicity of organic and inorganic mercury species in differentiated human neurons and human astrocytes. Journal of Trace Elements in Medicine and Biology 32:200-208. http://dx.doi.org/10.1016/j.jtemb.2015.06.008
Martins AC, Ke T, Bowman AB, Aschner M (2021) New insights on mechanisms underlying methylmercury-induced and manganese-induced neurotoxicity. Current Opinion in Toxicology 25:30-35. https://doi.org/10.1016/j.cotox.2021.03.002
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. Journal of Computational Chemistry16:2785-2791. https://doi.org/10.1002/jcc.21256
O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open Babel: An open chemical toolbox. Journal Cheminformatics 3:33. https://doi.org/10.1186/1758-2946-3-33
Pant D, Singh P (2014) Pollution due to hazardous glass waste. Environmental Science and Pollution Research 21(4):2414-2436. https://doi.org/10.1007/s11356-013-2337-y
Ribeiro CAO, Rouleau C, Pelletier E, Audet C, Tjalve H (1999) Distribution kinetics of dietary methylmercury in the artic charr (Salvelinus alpinus). Environmental Science & Technology 33:902–907. https://doi.org/10.1021/es980242n
Strange RW, Hough MA, Antonyuk SV, Hasnain SS (2012) Structural evidence for a copper-bound carbonate intermediate in the peroxidase and dismutase activities of superoxide dismutase. PLoS One 7(9):e44811. https://doi.org/10.1371/journal.pone.0044811.
Sun Y, Li Y, Rao J, Liu Z, Chen Q (2018) Effects of inorganic mercury exposure on histological structure, antioxidant status and immune response of immune organs in yellow catfish (Pelteobagrus fulvidraco). Journal Applied Toxicology 38(6):843-854. https://doi.org/10.1002/jat.3592
Suvarapu, Lakshmi Narayana, Seo, Young-Kyo and Baek, Sung-Ok (2013) Speciation and determination of mercury by various analytical techniques. Journal Analytical Chemistry, 32(3): 225-245. https://doi.org/10.1515/revac-2013-0003
Tan Q, Liu Z, Li H, Liu Y, Xia Z, Xiao Y, Usman M, Du Y, Bi H, Wei L (2018) Hormesis of mercuric chloride-human serum albumin adduct on N9 microglial cells via the ERK/MAPKs and JAK/STAT3 signaling pathways. Toxicology 408:62-69. https://doi.org/10.1016/j.tox.2018.07.001
Trisciuzzi, D, Alberga D, Leonetti F, Novellino E, Nicolotti, O, Mangiatordi GF (2018) Molecular Docking for Predictive Toxicology. Computational Toxicology1800:181–197. https://doi.org/10.1007/978-1-4939-7899-1_8
Trott, O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. Journal of Computational Chemistry 31(2):455-461. https://doi.org/10.1002/jcc.21334
Veiga MM, Hinton J, Lilly C. (1999). Mercury in Amazon: A Comprehensive Review with Special Emphasis on Bioaccumulation and Bioindicators. Proceeding of National Institute for Minamata Disease Japan. 19–39.
Zahir, F, Rizwi, S.J, Haq, S.K, Khan, R.H (2005) Low dose mercury toxicity and human health. Environmental Toxicology and Pharmacology 20(2):351-360. http://dx.doi.org/10.1016/j.etap.2005.03.007
Published
How to Cite
Issue
Section
License
Copyright (c) 2023 Journal of Education, Science and Health – JESH
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.